December 23, 2017

Events and jobs
Assistant Professor of Environmental Microbiology (Tenure-Track) – George Mason University – Fairfax, Virginia, USA
The George Mason University, Department of Environmental Science and Policy (ESP) is seeking an enthusiastic and energetic individual for a Tenure-Track Assistant Professor position in Molecular Environmental Microbiology to supplement existing departmental strengths in applied ecology, aquatic ecology, one health and conservation. This is a full-time, tenure-track position to begin August 2018.

Manager, QC Microbiology – Catalent Pharma Solutions, Inc. – Madison, Wisconsin, USA

Post-Doc – Microbiology & Immunology – Cornell University – Ithaca, NY, USA

Biological Sciences Full-Time Instructor (Microbiology Emphasis) – West Valley-Mission Community College District – Saratoga, CA, USA

General microbiome
Review: Building conventions for unconventional lymphocytes. – Lesley Pasman – Immunological Reviews (from September, but not posted before)

Pregnancy and early life
Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan – AOGS

Multi-site human microbiome
Review: The role of microbial amyloid in neurodegeneration. – Robert P Friedland – Plos Pathogens

Human respiratory microbiome
Review: Airway microbiome research: a modern perspective on surveillance cultures? – Damien Roux – Annals Of Translational Medicine

Human skin microbiome
Review: Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt? – Andrew McDowell – Microorganisms

Human oral microbiome
Ecological Balance of Oral Microbiota is Required to Maintain Oral Mesenchymal Stem Cell Homeostasis. – Yingying Su – Stem Cells (Dayton, Ohio)

Shift in the Subgingival Microbiome following Scaling and Root Planing in Generalized Aggressive Periodontitis. – Guojing Liu – Journal Of Clinical Periodontology

Human gut microbiome
Quinones are growth factors for the human gut microbiota. – Kathrin Fenn – Microbiome

Opinion: Microbiome-Germline Interactions and Their Transgenerational Implications. – Michael Elgart – Bioessays : News And Reviews In Molecular, Cellular And Developmental Biology

Review: Modeling metabolism of the human gut microbiome – Stefanía Magnúsdóttir – Current Opinion in Biotechnology

Microbial ecology
Opinion: Engineering microbial communities using thermodynamic principles and electrical interfaces. – Christian Zerfaß – Current Opinion In Biotechnology

Animal experiments
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. – Mads T F Damgaard – The Journal Of Nutritional Biochemistry

Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. – Yang Song – FEMS Microbiology Ecology

Impact of genistein on the gut microbiome of humanized mice and its role in breast tumor inhibition. – Bidisha Paul – Plos One

Tomato Powder Inhibits Hepatic Steatosis and Inflammation Potentially Through Restoring SIRT1 Activity and Adiponectin Function Independent of Carotenoid Cleavage Enzymes in Mice. – Cheng-Chung Li – Molecular Nutrition & Food Research

Faecal microRNAs: indicators of imbalance at the host-microbe interface? – G M Moloney – Beneficial Microbes

Modulation of the fecal microbiota in Sprague-Dawley rats using genetically modified and isogenic corn lines. – Penggao Li – Journal Of Agricultural And Food Chemistry

Sex-dependent impact of Roundup on the rat gut microbiome – Veronica L. Lozano – Toxicology Reports

Effects of garlic-supplemented diet on growth performance and intestinal microbiota of rainbow trout (Oncorhynchus mykiss) – Miray Etyemez Büyükdeveci – Aquaculture

Animal microbiome
Identification and chemical characterization of N acyl-homoserine lactone quorum sensing signals across sponge species and time. – Maya Britstein – FEMS Microbiology Ecology

Reptile-associated Borrelia species in the goanna tick (Bothriocroton undatum) from Sydney, Australia. – Jessica L Panetta – Parasites & Vectors

Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb – Antonio Palomba – Proteomes

Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets – Marc D. Auffret – Frontiers in Microbiology

Plant, root, and soil microbiome
Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter. – Bo Zhang – Scientific Reports

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation. – Tanzelle Oberholster – The Science Of The Total Environment

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. – Aylan K Meneghine – Plos One

Field study reveals core plant microbiota and relative importance of their drivers. – Kelly Hamonts – Environmental Microbiology

Enhanced arsenic uptake and polycyclic aromatic hydrocarbon (PAH)-dissipation using Pteris vittata L. and a PAH-degrading bacterium. – Lu Sun – The Science Of The Total Environment

Division of labor during biofilm matrix production – Anna Dragos – bioRxiv

Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots – Daniel Schlatter – Phytopathology

Long-term and legacy effects of manure application on soil microbial community composition – Yuting Zhang – Biology and Fertility of Soils

Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment – Yanxia Nie – Science of the Total Environment

Water and extremophile microbiome
Consequences of contamination on the interactions between phytoplankton and bacterioplankton. – Goni-Urriza Marisol – Chemosphere

Identification of active denitrifiers by DNA-Stable Isotope Probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer. – M Inés Bellini – FEMS Microbiology Ecology

The importance of filamentous cyanobacteria in the development of oxygenic photogranules. – Kim Milferstedt – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition. – Xiang-Yi Li – Journal Of The Royal Society, Interface (In freshwater metazoan Hydra vulgaris)

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces – Marion Pohlner – Frontiers in Microbiology

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics – Kristin Bergauer – PNAS (From November 2017, not posted before)

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes – Holly L. Sewell – mBio

Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone – Mandar Bandekar – Deep Sea Research Part II: Topical Studies in Oceanography

Review: Microalgae–bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage – Sudharsanam Abinandan – Applied Microbiology and Biotechnology

Built environment
Changes in bacterial and archaeal communities during the concentration of brine at the graduation towers in Ciechocinek spa (Poland) – Agnieszka Kalwasińska – Extremophiles

The Coal Seam Microbiome (CSMB) Reference Set, a lingua franca for the microbial coal-to-methane community – Silas H.W. Vick – International Journal of Coal Geology

Food microbiology
Review: Impact of nanosilver on gut microbiota: a vulnerable link. – Dinesh Kumar Dahiya – Future Microbiology

Probiotics / prebiotics
Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial. – T Nagino – Beneficial Microbes

Effect of tablets containing probiotic candidate strains on gingival inflammation and composition of the salivary microbiome: a randomised controlled trial. – M K Keller – Beneficial Microbes

Phages and viruses
Review: Inflammatory Bowel Disease’s Specific Changes of Enteric Mycobiota and Virome. – Yi Chu – Journal Of Digestive Diseases

Review: Phages of life – the path to pharma. – Amanda Forde – British Journal Of Pharmacology

Bioinformatics
Hybrid-denovo: A de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags. – Xianfeng Chen – Gigascience

** 3D molecular cartography using LC-MS facilitated by Optimus and ‘ili software. – Ivan Protsyuk – Nature Protocols **

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve fungal high throughput amplicon sequencing data – Jonathan M Palmer – bioRxiv

Multi-omics integration—a comparison of unsupervised clustering methodologies – Giulia Tini – Briefings in Bioinformatics

Review: Genome-scale metabolic networks in time and space – Ove Øyås – Current Opinion in Systems Biology

Techniques
Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization. – Benjamin Buysschaert – Cytometry. Part A : The Journal Of The International Society For Analytical Cytology

Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid – Tanya Prozorov – Journal of the Royal Society

Microbes in the news
Higher Numbers of 2 Bacteria Species Found in Sarcoidosis Patients, Study Finds – Janet Stewart – Sarcoidosis News

The Surprising Way Your Brain and Gut Are Connected – Julia Malacoff – Shape

Gut Bacteria May Influence Infant Intelligence – Batya Swift Yasgur – MedScape

What Humans Can Learn About Gut Health From Monkey ‘Huddling’ – Francesca Friday – Observer

How to keep your gut healthy over the holidays – Yella Hewings-Martin – Medical News Today

Studies Link Oral Microbiome to Cancers – Pam Harrison – MedPage

Bacteria Found Alive in Earth’s Most Extreme Environments for the First Time Hold Clues to Life on Other Planet – Sydney Pereira – Newsweek

Antibiotic resistance: ‘Sleeping’ bacteria that can survive drug treatment identified – Phys.Org

Bacteria-Basted Supertrees Are Sucking Pollution From Our Waste Sites – James Poulos – Good

Everything you know about toxic shock syndrome is probably wrong – Sara Chodosh – Popular Science

Microbes on the market
Direct-to-consumer DNA and microbiome test launched in Europe – PharmaPhorum

BiomX acquires RondinX to expand microbiome targets for IBD, liver disease – Jonathan Solomon – HealIO

DSM Acquires BioCare Copenhagen to Expand Gut Health Ingredients Portfolio with Probiotics – CISION

Sarcoidosis Industry Overview with Total Market Share and Distribution of Sarcoidosis for 7 MM for 2025 – Miltech

Global Human Microbiome Market Analysis, Share, Production, Growth, Trends and Forecast 2017 to 2022 – Arun P. – GeoPolMonitor

Global Microbiome Therapeutic Market Outlook – Johnson and Johnson, AB-Biotics, Vedanta Biosciences, AbbVie Inc – Kevin Harper – The News Columnist

Bacteria Hysteria
‘This is how the X-Men started’: Internet shocked by astronaut discovery of ‘alien bacteria’ on International Space Station – Sarah K. Burris – RawStory

Science, publishing, and career
Graduate Biomedical Science Education Needs a New Philosophy – Gundula Bosch – mBio

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November 28, 2017

Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.

Events and jobs

Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark

Human skin microbiome

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE

Human gut microbiome

Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv

Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology

Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer

Animal experiments

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology

Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports

Animal microbiome

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Plant, root, and soil microbiome

Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv

Water and extremophile microbiome

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences

Phages and viruses

Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research

Bioinformatics

Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology

More microbes

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports

Microbes in the news

Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org

Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress

Microbe threat to Mars – Andrew Masterson – Cosmos

Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist

Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health

CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News

Bacteria hysteria

Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee

Science, career, and publishing

Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv

November 27, 2017

Short digest today – with multiple reviews and papers on animal microbiomes, as well as an interesting art project!

Pregnancy and early life
First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk – Mohammed Monzoorul Haque – Scientific Reports

Human skin microbiome
Skin Colonization by Staphylococcus aureus Precedes the Clinical Diagnosis of Atopic Dermatitis in Infancy – Patrick Meylan – Journal of Investigative Dermatology

Human nearly-sterile sites
ReviewGut reactions: How the blood-brain barrier connects the microbiome and the brain – Aric F Logsdon – Experimental Biology and Medicine

Human gut microbiome
Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer – Susan Bullman – Science

Animal experiments
Resident Microbiome Disruption with Antibiotics Enhances Virulence of a Colonizing Pathogen – Courtney A. Thomason – Scientific Reports
# Using house finches!

Structure moderation of gut microbiota in liraglutide-treated diabetic male rats – Qian Zhang – Experimental Biology and Medicine

Volatile Oil from Amomi Fructus Attenuates 5-Fluorouracil-Induced Intestinal Mucositis – Ting Zhang – Frontiers in Pharmacology

Animal microbiome
Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Review: The Gastrointestinal Microbiome: A Review – P.C. Barko – Journal of Veterinary Internal Medicine

Plant, root, and soil microbiome
Metagenomic Approach to Identifying Foodborne Pathogens on Chinese cabbage – Daeho Kim – Journal of Microbiology and Biotechnology

Review: Trade, Diplomacy, and Warfare: The Quest for Elite Rhizobia Inoculant Strains – Alice Checcucci – Frontiers in Microbiology

Water and extremophile microbiome
What intrinsic and extrinsic factors explain the stoichiometric diversity of aquatic heterotrophic bacteria? – Casey M Godwin – ISMEJ

Antagonistic bacteria disrupt calcium homeostasis and immobilize algal cells – Prasad Aiyar – Nature Communications

Probiotics / prebiotics / antibiotics
Review: Existing and investigational therapies for the treatment of Clostridium difficile infection: A focus on narrow spectrum, microbiota-sparing agents – H.G. Maxwell-Scott – Médecine et Maladies Infectieuses

Techniques
Book chapterComputational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design – Mohammad Mazharul Islam – Synthetic Metabolic Pathways

Microbes in the news
Mothers’ gut bacteria could impact future health of children: new findings – Brigid O’Connell – Herald Sun
# Part of the ENvironmental Determinants of Islet Autoimmunity (ENDIA) study

NASA fires E. coli bacteria into space to see if antibiotic resistance increases in zero gravity – Patricia Grannum – Inquisitr

Mouthwash Kills Mouth Bacteria But May Increase Risk For Diabetes – Allan Adamson – Tech Times

Artist’s feces work contributes to gut-busting research – The Japan Times

Alarm on milk with high levels of bacteria – Angela Oketch – Daily Nation
# In Kenya

Potato Bugs, Weeds, and Harmful Bacteria – Terry Mejdrich – Grand Rapids MN Herald Review

Bacteria Hysteria
Here’s Why You Should Never, Ever Share Earbuds with Anyone – Brittany Gibson – Reader’s Digest
# The article itself makes sense, but the title…

November 17, 2017

Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour, Microbiome

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology

Bioinformatics

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ

Techniques

Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

July 31, 2017

Short digest today, with many articles from Applied and Environmental Microbiology (AEM)!

General microbiome
Review: Bacterial infection increases risk of carcinogenesis by targeting mitochondria – Jesper A.B. Strickertsson – Seminars in Cancer Biology

Pregnancy and early life
Iron in Micronutrient Powder Promotes an Unfavorable Gut Microbiota in Kenyan Infants – Minghua Tang – Nutrients

Multi-site human microbiome
Review: Role of uremic toxin indoxyl sulfate in the progression of cardiovascular disease – Huichang Gao – Life Sciences

Human gut microbiome
The sortase-dependent fimbriome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue – Christian Milani – Applied and Environmental Microbiology

Repression of Salmonella host cell invasion by aromatic small molecules from the human fecal metabolome – Rafael J.M. Peixoto – Applied and Environmental Microbiology

Animal experiments
Antibiotic-Induced Microbiota Dysbiosis Impairs Neuromuscular Function in Juvenile Mice – Valentina Caputi – British Journal of Pharmacology

10-oxo-12(Z)-octadecenoic acid, a linoleic acid metabolite produced by gut lactic acid bacteria, enhances energy metabolism by activation of TRPV1 – Minji Kim – FASEB

Water and extremophile microbiome
Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Community Diversity – Cuina Bu – Scientific Reports

Built environment
Phage-host associations in a full-scale activated sludge plant during sludge bulking – Ruyin Liu – Applied Microbiology and Biotechnology

Phages and viruses
Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures – Veronica Barragan – Applied and Environmental Microbiology

Microbes in the news
Flesh-Eating Vibrio Can Come From Cleaning Fish…As Well As Swimming – Judy Stone – Forbes

Burp! Singapore scientists hope for probiotic beer hit – Reuters – Deccan Chronicle

Bacteria Hysteria
Blowing out birthday candles increases bacteria on cake’s icing – study –
Daily Mail

Deadly mix: Brewing faecal bacteria in your coffee cup? – Jagruti Verma – Deccan Chronicle

July 16, 2017

Events and jobs
Postdoctoral Fellow – Astrobiology – University of Florida

Microbiology Laboratory Manager – Cranleigh Scientific, Northamptonshire, England

Human respiratory microbiome
Review: Microbiome in chronic obstructive pulmonary disease – Eduard Monso – Annals of Translational Medicine

Monitoring clinical and microbiological evolution of a cystic fibrosis patient over 26 years: experience of a Brazilian CF Centre – Cassiana da Costa Ferreira Leite – BMC Pulmonary Medicine

Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplantation

Human oral microbiome
Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity – E. Xiao – Cell Host and Microbe

Microbiome of peri-implantitis affected and healthy dental sites in patients with a history of chronic periodontitis – Danae Apatzidou – Archives of Oral Biology

Human gut microbiome
Review: Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Determination of certain bacterial groups in gut microbiota and endotoxin levels in patients with nonalcoholic steatohepatitis – Ceren Özkul – The Turkish Journal of Gastroenterology

Animal experiments
Meat and bone meal as partial replacement of fishmeal in diets for gilthead sea bream (Sparus aurata) juveniles: Diets digestibility, digestive function, and microbiota modulation – Sara Moutinho – Aquaculture

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Mohamed Zeineldin – Veterinary Microbiology

Animal microbiome
Effects of chromium(III) on enzyme activities and bacterial communities during swine manure composting – Yanan Yin – Bioresource Technology

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites – R. A. Arango – Environmental Entomology

Oral Disease and Microbiota in Free-roaming cats – Ana Whyte – Topics in Companion Animal Medicine

Plant, root, and soil microbiome
Investigating the durable effect of the hot water treatment used in nurseries on pathogenic fungi inhabiting grapevine wood and involved in Grapevine Trunk Diseases – Emilie Bruez – Crop Protection

Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety – José Rodrigo Mendoza – Crop Protection

The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland – Hidetoshi Urakawa – Ecological Engineering

Water and extremophile microbiome
The Other Microeukaryotes of the Coral Reef Microbiome – T.D. Ainsworth – Trends in Microbiology

Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area – Stefan Thiele – Marine Genomics

Built environment
Stimulation effect of electric current density (ECD) on microbial community of a three dimensional particle electrode coupled with biological aerated filter reactor (TDE-BAF) – Yan Feng – BioResource Technology

Food microbiology
Review: Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective – Harsh Mathur – Frontiers in Microbiology

Review: Low FODMAP Diet in the Treatment of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis – Dania Schumann – Nutrition

Macrophages treated with non-digestible polysaccharides reveal a transcriptionally unique phenotype – Yongfu Tang – Journal of Functional Foods

Microbial Ecology
Interplay between antibiotic efficacy and drug-induced lysis underlie enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

A phylogenetic and evolutionary analysis of antimycin biosynthesis – Rebecca Joynt – bioRxiv

Probiotics / prebiotics
Review: Prenatal and postnatal administration of prebiotics and probiotics – Kristin Sohn – Seminars in Fetal and Neonatal Medicine

Techniques
Phototrophic microorganisms in the symbiotic communities of Baikal sponges: Diversity of psbA gene (encoding D1 protein of photosystem II) sequences – OV Kaluzhnaya – Mol Biol (Mosk)
Unfortunately, this article is in Russian and I cannot access the original. The abstract was interesting though, the goal of the study is to determine whether psbA sequences can be used as a marker for phototrophic organisms.

New sequences
Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics – F. Cadoret – New Microbes and New Infections

Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India – Sara Jones – Genome Announcements

Phoenicibacter massiliensis‘ gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman – M. Bilen – New Microbes and New Infections

Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery – Amine Namouchi – BMC Genomics

Microbes in the news 
** Mini-Metagenomics Leads to Microbial Discovery – Abby Olena – The Scientist
Refers to Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Brian Yu – ELife **

APC Microbiome Institute appoints Spinning Clock to Mind Your Microbes brief – Andy Black – The Drum
An app for kids to learn about the microbiome!

Microbial diversity: ‘key benchmark in the coming Third Wave cosmetic revolution’ – Lucy Whitehouse – Cosmetics Design

Novel bacterial physiology identified in the creation of biofilms – Science Daily

Physicists Just Found a Way to Spin Teeny Tiny Robot Motors With Bacteria – Gemma Conroy – Science Alert

New bacteria being developed for cheese may save industry $10m a year, researchers say – Melanie Vujkovic – ABC

Bacteria-infected mosquitoes are coming to Fresno – but it’s a good thing! – Bryant-Jon Anteola – Fresno Bee

BYU student overcomes flesh-eating bacteria to compete on ‘American Ninja Warrior’ – Braley Dodson – Daily Herald

Bacteria Actively Drive Development of Colorectal Cancer – Newswise
Looking at Streptococcus gallolyticus and its ability to promote colorectal cancer in cell culture, animal models, and human tissue.

Bacteria Hysteria
How surgeons can stop the spread of germs by operating NAKED instead of wearing surgical gowns – Colin Fernandez – Daily Mail

July 2, 2017

Events and jobs

Post-doc in High-Throughput Metagenomics – University of Cambridge

Microbes in the news

Before you head out to the beach this weekend, check bacteria levels – ABC News

Oil-Munching Bacteria Helped Clean Up the Deepwater Horizon Oil Spill –  Cynthia Wallentine, Invisiverse

Bacteria Hysteria

Here’s What the Gross Bacteria on Your Expired Makeup Really Looks Like – Erin Reimel, Glamour Magazine